The timeline is as follows:
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Trinity was animated to open and present the missile only when given an attack command.
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People used this to cause enemy nukes to explode on launch by watching the Trinity and then moving a unit in the way.
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The repository says I did this with a Dirtbag in 2011 (the Trinity survived, and nukes not dealing self-damage was fixed shortly afterwards).
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Firepluk started using Athenas to block nukes frequently.
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Someone came up with the technique of giving Trinity an attack command then a wait command, making the animation stay in the launch position. This allows nukes to be launched with no wind-up.
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Someone (possibility the same someone) made a widget to do this automatically.
At this point the "units should use their abilities intelligently" clause of the design was tripped, resulting in the following. The main options were:
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Trinity should not be primable. An attack command would lead to an uninterruptible attack animation and launch. This makes the widget impossible.
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Trinity should be force primed. The nuke would poke out upon stockpile completion and can be launched instantly. This force-implements the widget.
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Some combination of the previous two options for the sake of 'ability realism' and 'decisions'.
Option 1 raises many design and usability questions. What if the player wants to cancel the launch? Can it be retargeted during the animation? Does reclaiming or stunning the Trinity cancel the launch? The UI would be terrible and really not worth the trouble for enabling a niche trick.
Option 2 was picked because it has the added benefit of showing scouts whether the Trinity has a nuke ready to go, which is a nice extra bit of interactivity. Letting people choose between a vulnerability to Athena or a vulnerability to scouting (ie Option 3) seemed like far too small of a choice to be worth implementing*.
To finish the timeline:
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Option 2 was implemented.
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The Athena nuke blocking strategy was essentially dead as launches could not longer be anticipated from an animation.
*To get a feel for how small this choice is, remember that Solars have a Unit AI state toggle and that Dominatrix can be set to automatically kill captured units. Solars have full control over their ability to open or close, Trinity does not.